title: Translocation dynamics of tRNA-mRNA in the ribosome.
abstract: Translocation of tRNA-mRNA complex in the ribosome is an essential step in the elongation cycle of protein synthesis. However, some important issues concerning the molecular mechanism of the tRNA-mRNA translocation catalyzed by EF-G.GTP or by EF-G.GDPNP remain controversial. For example, can EF-G.GTP selectively bind to the hybrid pretranslocation state or bind to both the non-rotated pretranslocation and the hybrid pretranslocation states? Does the greater potency of EF-G in the presence of GTP rather than GDPNP in facilitating translocation derive from the effects on transition from the classical non-rotated to hybrid state (the first step of the translocation) or on transition from the hybrid to posttranslocation state (the second step)? Here, based on our proposed model, we study theoretically the dynamics of the tRNA-mRNA translocation through the ribosome catalyzed by EF-G.GTP and by EF-G.GDPNP. By comparing our theoretical results with the available experimental data, we show that EF-G.GTP can also bind to the classical non-rotated pretranslocation state and the greater potency of GTP hydrolysis in facilitating translocation of tRNA-mRNA complex derives from its effects on the second step of the translocation process.
authors.affiliation: Key Laboratory of Soft Matter Physics and Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China. Electronic address: pxie@aphy.iphy.ac.cn.
authors.forename: Ping
authors.initials: P
authors.lastname: Xie
mesh_terms: D000465:Algorithms; D006160:Guanosine Triphosphate / Q000378:metabolism; D007700:Kinetics; D020653:Peptide Elongation Factor G / Q000378:metabolism; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000378:metabolism*; D012343:RNA, Transfer / Q000378:metabolism*; D012270:Ribosomes / Q000378:metabolism*
chemical_list: D020653:Peptide Elongation Factor G; D012333:RNA, Messenger; D006160:Guanosine Triphosphate; D012343:RNA, Transfer
keywords: Hybrid state; Ribosome; Translation; Translocation; tRNA–mRNA